If you're not familiar with where the Sacramento-San Joaquin Delta is or why it's so important to the state, you're not alone. Polls show most Californians have never heard of it.

This relatively small part of California plays a crucial role in the state's water supply. And, as might be expected, it's become ground zero for a decades-long water war involving cities, farmers and fish. This year, the state is taking on an ambitious planning effort to break that deadlock.

Re-plumbing California

The reason the Delta has this starring role is thanks to a basic geography problem. Almost all of the state's water is found in the top third of the state. Most of the population lives in the bottom two-thirds of the state.

This issue was painfully obvious to state planners a century ago. The Central Valley promised rich soil for farmers, but had little rainfall. They knew for California to grow, they had to move water to drier parts of the state.

The Delta is where California's two largest rivers come together, carrying runoff from the Sierra Nevada Mountains. To water planners, it looked like the perfect place to tap into. California began building water infrastructure at a massive scale.

Water is exported out of the Delta primarily through two large pumping plants near Tracy, about 60 miles east of San Francisco. Each moves millions of gallons of water a minute. From there, the water rushes into concrete canals that reach Los Angeles, Silicon Valley and millions of acres of farmland.

This 700-mile system has made California the state it is today. But it's come with a cost…

Chart: How We Use Delta WaterDescription: Water that flows through Delta is pumped hundreds of miles across California. The Central Valley Project sends water to farms, while the State Water Project reaches Los Angeles and Silicon Valley, as well as Central Valley farmland. The Bay Area also receives water from the North Bay Aqueduct and the Contra Costa Canal. In some years, as much as 50 percent of the water that flows through the Delta is exported.Tags: water, delta, diversions, san francisco bay delta, fishing, salmon, smelt, exports, CCWD, kqed, quest, Delta-Mendota Canal. BDCP, farmingAuthor: charts powered by iCharts

An Ecosystem in Decline

On a boat in the western Delta, environmental scientist Julio Adib-Samii and team from California's Department of Fish and Game pull in a long fishing net.

A Delta smelt.

"Well, we have an adult Delta smelt," he says, holding a small, silver endangered fish that smells distinctly like a cucumber.

Fish and Game scientists have done these monthly fish surveys for decades. But starting in 2002, they noticed something strange. Where they once caught a lot of Delta smelt, now, they weren't catching any. The population had crashed, as well as populations of striped bass, threadfin shad, longfin smelt and Chinook salmon. In 2008, the commercial salmon fishery shut down completely for two years.

"Their decline is an indication of a changing environment and place they didn't evolve to be in," says Adib-Samii.

The Delta was once a massive tidal marsh, full of winding channels that spread out like capillaries. After the Gold Rush, settlers put up levees to create low-lying islands for farming. Ninety-seven percent of the historic wetlands were lost.

Multiple Stressors, One Big Question

"We've converted almost every scrap of habitat in the Delta to farmland and we need to return some of that to habitat," says Barry Nelson, senior policy analyst with the Natural Resources Defense Council. The ecosystem has also been hit by pollution, invasive species – and by the pumping plants.

"The pumps in the south Delta are so powerful that they literally reverse the direction of flow. It's very easy for those fish to follow that water and get sucked right into the pumps," says Nelson. A few years ago, federal wildlife agencies issued decisions requiring the pumping to slow down during certain times of year to protect fish.

This brings us to the central debate in the Delta: how much water should be pumped out and how much should be left for fish?

"There's a limit to the amount of water you can pump from the Delta ecosystem and in the last decade it's become incredibly clear that we've exceeded that, and we've exceeded it by a lot," says Nelson.

Not everyone agrees. "There is, you know, always going to be shortages. But there's also a lot of years when we have absolutely plenty of water in the system to meet the reasonable needs that are out there," says Jason Peltier with Westlands Water District, an agricultural area in the San Joaquin Valley that depends on Delta water. He says limits on pumping have hurt the district's farmers.

"You can't get a loan to farm unless you can show the banker what water you have. And they don't have a lot of confidence in going to their bankers," says Peltier.

The battle over the environmental rules went to the courts. "There was lawsuit after lawsuit," says John Laird, California's Secretary for Natural Resources. "It got to the point that it made much more sense to look at the entire Delta as a whole."

A New Attempt at Progress

Laird's agency is trying to reach a compromise with the Bay Delta Conservation Plan. The 10,000-page plan calls for a new way to pump water out of the Delta, through what's commonly known as the peripheral canal. Huge tunnels would take water from further upstream, bypassing the Delta, which supporters say would make the water supply more reliable.

This isn't a new idea. In 1982, California voters defeated a similar plan. "The real debate is not the tunnel itself. It's how much water and when can it flow through the tunnel," says Laird.

The massive project could harm the Delta's endangered species, but Laird says they'll restore thousands of acres of wetlands to compensate. California voters would be on the hook for that cost, while the $12 billion tunnel would be paid for by water users.

It's a tough sell but, according to Laird, a necessary one since climate change will make the state's water supply more unpredictable. The agency will release a full draft of the plan in July.

Lauren is a radio reporter covering environment, water, and energy for KQED Science. As part of her day job, she has scaled Sierra Nevada peaks, run from charging elephant seals, and desperately tried to get her sea legs - all in pursuit of good radio. Her work has appeared on Marketplace, Living on Earth, and NPR's Morning Edition and All Things Considered. You can find her on Twitter at @lesommer.